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PDBsum entry 3m99
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Transcription
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PDB id
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3m99
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Contents |
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422 a.a.
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89 a.a.
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91 a.a.
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84 a.a.
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* Residue conservation analysis
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PDB id:
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Transcription
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Title:
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Structure of the ubp8-sgf11-sgf73-sus1 saga dub module
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Structure:
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Ubiquitin carboxyl-terminal hydrolase 8. Chain: a. Synonym: ubiquitin thioesterase 8, ubiquitin-specific-processing protease 8, deubiquitinating enzyme 8. Engineered: yes. Saga-associated factor 11. Chain: b. Synonym: 11 kda saga-associated factor. Engineered: yes.
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Source:
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Saccharomyces cerevisiae. Brewer's yeast,lager beer yeast,yeast. Organism_taxid: 4932. Gene: ubp8, ym9959.05, ymr223w. Expressed in: escherichia coli. Expression_system_taxid: 562. Yeast. Gene: sgf11, ypl047w. Gene: sus1, ybr111w-a.
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Resolution:
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2.70Å
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R-factor:
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0.237
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R-free:
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0.300
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Authors:
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A.Kohler,E.Zimmerman,M.Schneider,E.Hurt,N.Zheng
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Key ref:
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A.Köhler
et al.
(2010).
Structural basis for assembly and activation of the heterotetrameric SAGA histone H2B deubiquitinase module.
Cell,
141,
606-617.
PubMed id:
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Date:
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21-Mar-10
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Release date:
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05-May-10
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PROCHECK
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Headers
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References
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P50102
(UBP8_YEAST) -
Ubiquitin carboxyl-terminal hydrolase 8 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
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Seq:
Struc:
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471 a.a.
422 a.a.
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Q03067
(SGF11_YEAST) -
SAGA-associated factor 11 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
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Seq:
Struc:
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99 a.a.
89 a.a.
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Enzyme class:
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Chain A:
E.C.3.4.19.12
- ubiquitinyl hydrolase 1.
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Reaction:
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Thiol-dependent hydrolysis of ester, thiolester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).
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Cell
141:606-617
(2010)
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PubMed id:
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Structural basis for assembly and activation of the heterotetrameric SAGA histone H2B deubiquitinase module.
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A.Köhler,
E.Zimmerman,
M.Schneider,
E.Hurt,
N.Zheng.
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ABSTRACT
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Deubiquitinating enzymes (DUBs) regulate diverse cellular functions by cleaving
ubiquitin from specific protein substrates. How their activities are modulated
in various cellular contexts remains poorly understood. The yeast deubiquitinase
Ubp8 protein is recruited and activated by the SAGA complex and, together with
Sgf11, Sus1, and Sgf73, forms a DUB module responsible for deubiquitinating
histone H2B during gene expression. Here, we report the crystal structure of the
complete SAGA DUB module, which features two functional lobes structurally
coupled by Sgf73. In the "assembly lobe," a long Sgf11 N-terminal helix is
clamped onto the Ubp8 ZnF-UBP domain by Sus1. In the "catalytic lobe," an Sgf11
C-terminal zinc-finger domain binds to the Ubp8 catalytic domain next to its
active site. Our structural and functional analyses reveal a central role of
Sgf11 and Sgf73 in activating Ubp8 for deubiquitinating histone H2B and
demonstrate how a DUB can be allosterically regulated by its nonsubstrate
partners.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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K.K.Lee,
M.E.Sardiu,
S.K.Swanson,
J.M.Gilmore,
M.Torok,
P.A.Grant,
L.Florens,
J.L.Workman,
and
M.P.Washburn
(2011).
Combinatorial depletion analysis to assemble the network architecture of the SAGA and ADA chromatin remodeling complexes.
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Mol Syst Biol,
7,
503.
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L.Frappier,
and
C.P.Verrijzer
(2011).
Gene expression control by protein deubiquitinases.
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Curr Opin Genet Dev,
21,
207-213.
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M.P.Luna-Vargas,
A.C.Faesen,
W.J.van Dijk,
M.Rape,
A.Fish,
and
T.K.Sixma
(2011).
Ubiquitin-specific protease 4 is inhibited by its ubiquitin-like domain.
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EMBO Rep,
12,
365-372.
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PDB code:
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J.Bonnet,
Y.H.Wang,
G.Spedale,
R.A.Atkinson,
C.Romier,
A.Hamiche,
W.W.Pijnappel,
H.T.Timmers,
L.Tora,
D.Devys,
and
B.Kieffer
(2010).
The structural plasticity of SCA7 domains defines their differential nucleosome-binding properties.
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EMBO Rep,
11,
612-618.
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
code is
shown on the right.
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